Allow me to throw one more suggestion out that I mentioned in another thread.
I too suddenly started experiencing seeing 64-bit plugins missing. In my case, it was only a select number of 64-bit plugins, not ALL (*).. so it may be a different problem than yours. Do you separate your 32-bit install and your 64-bit installs in different folders? If so, check your VST Plugins Path setting in Reaper and put your 64-bit folder to the end of the list of folders and see if that helps. That somewhat solved my problem, although in my case all it did was now cause some 32-bit versions to not load. I actually like this problem though, because it only does this for plugins where the 64-bit version is installed (and working) too. So, less clutter in my plugins list, as I don't really want to see 32-bit plugins unless I have no 64-bit plugin.
Anyways, in my case, my problem happened after I uninstalled every single plugin (via add/remove programs) and the removed one of my drives, and replaced it with a brand new SSD. Reaper seems to be the issue in this case though, as I installed Reason and it found the plugins fine. Anyways, once I moved my 64-bit path to the end of the plugins path, it found the 64bit versions (but now doesn't show some 32 bit versions). I'm going to do some more experimenting later to see if I can fix my problem a little better. Will share if I find a fix.
(*) - the plugins missing were the ones where 32 bit and 64 bit file were named the same. I had them installed in separate folders, I had these folders in my Plugins Path, and I was running 64-bit Reaper... so none of the usual "gotchas" were the problem here.
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